MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : dimp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b2066 b1241 b0351 b4384 b2744 b0871 b2407 b3236 b3962 b1982 b2498 b3616 b3589 b3946 b2210 b0825 b4267 b4388 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b0325 b0508 b4266 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.493550 (mmol/gDw/h)
  Minimum Production Rate : 0.535025 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.315377
  EX_o2_e : 280.047379
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.472060
  EX_pi_e : 1.011106
  EX_so4_e : 0.124286
  EX_k_e : 0.096338
  EX_mg2_e : 0.004282
  EX_ca2_e : 0.002569
  EX_cl_e : 0.002569
  EX_cu2_e : 0.000350
  EX_mn2_e : 0.000341
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992073
  EX_h2o_e : 549.821112
  EX_co2_e : 30.903185
  EX_acald_e : 1.742917
  Auxiliary production reaction : 0.535025
  EX_ade_e : 0.000332
  DM_mththf_c : 0.000221
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

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Last updated: 21-Sep-2023
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